The influence of the metal cations and microhydration on the reaction trajectory of the N3 ↔ O2 thymine proton transfer: Quantum mechanical study

This study involves the intramolecular proton transfer (PT) process on a thymine nucleobase between N3 and O2 atoms. We explore a mechanism for the PT assisted by hexacoordinated divalent metals cations, namely Mg2+, Zn2+, and Hg2+. Our results point out that this reaction corresponds to a two‐stage...

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Published in:	Journal of computational chemistry Vol. 38; no. 31; pp. 2680 - 2692
Main Authors:	Šebesta, Filip, Brela, Mateusz Z, Diaz, Silvia, Miranda, Sebastian, Murray, Jane S, Gutiérrez‐Oliva, Soledad, Toro‐Labbé, Alejandro, Michalak, Artur, Burda, Jaroslav V
Format:	Journal Article
Language:	English
Published:	United States Wiley Subscription Services, Inc 05.12.2017
Subjects:	Cations chemical potential Computational chemistry DFT Ions Ligands Mercury (metal) Molecular chemistry Nuclei proton transfer Protons Quantum mechanics reaction coordinate Thymine reaction coordinate proton transfer DFT chemical potential thymine
ISSN:	0192-8651, 1096-987X, 1096-987X
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Abstract	This study involves the intramolecular proton transfer (PT) process on a thymine nucleobase between N3 and O2 atoms. We explore a mechanism for the PT assisted by hexacoordinated divalent metals cations, namely Mg2+, Zn2+, and Hg2+. Our results point out that this reaction corresponds to a two‐stage process. The first involves the PT from one of the aqua ligands toward O2. The implications of this stage are the formation of a hydroxo anion bound to the metal center and a positively charged thymine. To proceed to the second stage, a structural change is needed to allow the negatively charged hydroxo ligand to the N3 proton, which represents the final product of the PT reaction. In the presence of the selected hexaaqua cations, the activation barrier is at most 8 kcal/mol. © 2017 Wiley Periodicals, Inc. Intramolecular proton transfer (PT) process on thymine nucleobase between N3 and O2 atoms is explored in presence of hexacoordinated divalent metals cations Mg2+, Zn2+, and Hg2+. This PT proceeds as a two stages process. The first step involves the PT from one of the aqua ligands toward O2. The second stage is connected with the N3‐proton ion. In the presence of the hexaaqua‐cations, the activation barrier is at most 8 kcal/mol.
AbstractList	This study involves the intramolecular proton transfer (PT) process on a thymine nucleobase between N3 and O2 atoms. We explore a mechanism for the PT assisted by hexacoordinated divalent metals cations, namely Mg2+, Zn2+, and Hg2+. Our results point out that this reaction corresponds to a two‐stage process. The first involves the PT from one of the aqua ligands toward O2. The implications of this stage are the formation of a hydroxo anion bound to the metal center and a positively charged thymine. To proceed to the second stage, a structural change is needed to allow the negatively charged hydroxo ligand to the N3 proton, which represents the final product of the PT reaction. In the presence of the selected hexaaqua cations, the activation barrier is at most 8 kcal/mol. © 2017 Wiley Periodicals, Inc. Intramolecular proton transfer (PT) process on thymine nucleobase between N3 and O2 atoms is explored in presence of hexacoordinated divalent metals cations Mg2+, Zn2+, and Hg2+. This PT proceeds as a two stages process. The first step involves the PT from one of the aqua ligands toward O2. The second stage is connected with the N3‐proton ion. In the presence of the hexaaqua‐cations, the activation barrier is at most 8 kcal/mol. This study involves the intramolecular proton transfer (PT) process on a thymine nucleobase between N3 and O2 atoms. We explore a mechanism for the PT assisted by hexacoordinated divalent metals cations, namely Mg2+ , Zn2+ , and Hg2+ . Our results point out that this reaction corresponds to a two-stage process. The first involves the PT from one of the aqua ligands toward O2. The implications of this stage are the formation of a hydroxo anion bound to the metal center and a positively charged thymine. To proceed to the second stage, a structural change is needed to allow the negatively charged hydroxo ligand to abstract the N3 proton, which represents the final product of the PT reaction. In the presence of the selected hexaaqua cations, the activation barrier is at most 8 kcal/mol. © 2017 Wiley Periodicals, Inc.This study involves the intramolecular proton transfer (PT) process on a thymine nucleobase between N3 and O2 atoms. We explore a mechanism for the PT assisted by hexacoordinated divalent metals cations, namely Mg2+ , Zn2+ , and Hg2+ . Our results point out that this reaction corresponds to a two-stage process. The first involves the PT from one of the aqua ligands toward O2. The implications of this stage are the formation of a hydroxo anion bound to the metal center and a positively charged thymine. To proceed to the second stage, a structural change is needed to allow the negatively charged hydroxo ligand to abstract the N3 proton, which represents the final product of the PT reaction. In the presence of the selected hexaaqua cations, the activation barrier is at most 8 kcal/mol. © 2017 Wiley Periodicals, Inc. This study involves the intramolecular proton transfer (PT) process on a thymine nucleobase between N3 and O2 atoms. We explore a mechanism for the PT assisted by hexacoordinated divalent metals cations, namely Mg 2+ , Zn 2+ , and Hg 2+ . Our results point out that this reaction corresponds to a two‐stage process. The first involves the PT from one of the aqua ligands toward O2. The implications of this stage are the formation of a hydroxo anion bound to the metal center and a positively charged thymine. To proceed to the second stage, a structural change is needed to allow the negatively charged hydroxo ligand to abstract the N3 proton, which represents the final product of the PT reaction. In the presence of the selected hexaaqua cations, the activation barrier is at most 8 kcal/mol. © 2017 Wiley Periodicals, Inc. This study involves the intramolecular proton transfer (PT) process on a thymine nucleobase between N3 and O2 atoms. We explore a mechanism for the PT assisted by hexacoordinated divalent metals cations, namely Mg , Zn , and Hg . Our results point out that this reaction corresponds to a two-stage process. The first involves the PT from one of the aqua ligands toward O2. The implications of this stage are the formation of a hydroxo anion bound to the metal center and a positively charged thymine. To proceed to the second stage, a structural change is needed to allow the negatively charged hydroxo ligand to abstract the N3 proton, which represents the final product of the PT reaction. In the presence of the selected hexaaqua cations, the activation barrier is at most 8 kcal/mol. © 2017 Wiley Periodicals, Inc. This study involves the intramolecular proton transfer (PT) process on a thymine nucleobase between N3 and O2 atoms. We explore a mechanism for the PT assisted by hexacoordinated divalent metals cations, namely Mg2+, Zn2+, and Hg2+. Our results point out that this reaction corresponds to a two-stage process. The first involves the PT from one of the aqua ligands toward O2. The implications of this stage are the formation of a hydroxo anion bound to the metal center and a positively charged thymine. To proceed to the second stage, a structural change is needed to allow the negatively charged hydroxo ligand to abstract the N3 proton, which represents the final product of the PT reaction. In the presence of the selected hexaaqua cations, the activation barrier is at most 8 kcal/mol. © 2017 Wiley Periodicals, Inc.
Author	Michalak, Artur Murray, Jane S Miranda, Sebastian Gutiérrez‐Oliva, Soledad Šebesta, Filip Burda, Jaroslav V Toro‐Labbé, Alejandro Brela, Mateusz Z Diaz, Silvia
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Snippet	This study involves the intramolecular proton transfer (PT) process on a thymine nucleobase between N3 and O2 atoms. We explore a mechanism for the PT assisted...
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SubjectTerms	Cations chemical potential Computational chemistry DFT Ions Ligands Mercury (metal) Molecular chemistry Nuclei proton transfer Protons Quantum mechanics reaction coordinate Thymine
Title	The influence of the metal cations and microhydration on the reaction trajectory of the N3 ↔ O2 thymine proton transfer: Quantum mechanical study
URI	https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.24911 https://www.ncbi.nlm.nih.gov/pubmed/28925001 https://www.proquest.com/docview/1954789716 https://www.proquest.com/docview/1940598200
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